Acyl Type Research Articles

A Directed Evolution System for Lysine Deacetylases.

Lysine acetylation is a ubiquitous modification permeating the proteomes of organisms from all domains of life. Lysine deacetylases (KDACs) reverse this modification by following two fundamentally different enzymatic mechanisms, which differ mainly by the need for NAD+ as stoichiometric co-substrate. KDACs are often found as catalytic subunit in protein complexes involved in cell cycle regulation, chromatin organization and transcription. Their promiscuity with respect to sequence context and type of lysine acylation convolutes the network of functional and physical connections.Here we present an efficient selection method for KDACs in E. coli, which allows for the creation of acyl-type specific KDAC variants, which greatly facilitate the investigation of their physiological function . The selection system builds on the incorporation of acylated lysines by genetic code expansion in reporter enzymes with essential lysine residues. We describe the creation of KDAC mutant libraries by saturation mutagenesis of active site residues, the isolation of individual mutants from this library using the selection system, and their biochemical characterization with acylated firefly luciferase.

Micromonospora pelagivivens sp. nov., a new species of the genus Micromonospora isolated from deep-sea sediment in Japan.

A novel marine actinomycete, designated strain KJ-029T, was isolated from a marine sediment sample (water depth of 226 m) in Kagoshima, Japan. 16S rRNA gene sequence analysis revealed that the new isolate was most closely related to Micromonospora craniellae LHW 63014T (99.3 % similarity). Phylogenetic analyses of the genus Micromonospora based on 16S rRNA gene sequences showed that strain KJ-029T was clustered with Micromonospora craniellae LHW 63014T and Micromonospora endophytica 202201T. However, digital DNA-DNA hybridization analyses presented low levels of relatedness in the range of 24.8-32.9 % between strain KJ-029T and the above closely related strains. The novel strain contained meso-diaminopimelic acid and 3-OH-diaminopimelic acid, d-glutamic acid, glycine and d-alanine in the cell-wall peptidoglycan. The acyl type of the peptidoglycan was glycolyl and mycolic acids were absent. The major menaquinone was MK-9(H4). The whole-cell sugars consisted of glucose, mannose, xylose and ribose. Phosphatidylethanolamine was detected as the major phospholipid and corresponded to phospholipid type II. The predominant cellular fatty acid was iso-C16 : 0. The DNA G+C content of the genomic DNA was 71.5 mol%. Based on the present polyphasic study, strain KJ-029T represents a novel species of the genus Micromonospora, for which the name Micromonospora pelagivivens sp. nov. is proposed. The type strain is KJ-029T (=NBRC 113519T=TBRC 9233T).

Evolved, Selective Erasers of Distinct Lysine Acylations.

Lysine acylations, a family of diverse protein modifications varying in acyl‐group length, charge, and saturation, are linked to many important physiological processes. Only a small set of substrate‐promiscuous lysine acetyltransferases and deacetylases (KDACs) install and remove this vast variety of modifications. Engineered KDACs that remove only one type of acylation would help to dissect the different contributions of distinct acylations. We developed a bacterial selection system for the directed evolution of KDACs and identified variants up to 400 times more selective for butyryl‐lysine compared to crotonyl‐lysine. Structural analyses revealed that the enzyme adopts different conformational states depending on the type of acylation of the bound peptide. We used the butyryl‐selective KDAC variant to shift the cellular acylation spectrum towards increased lysine crotonylation. These new enzymes will help in dissecting the roles of different lysine acylations in cell physiology.

Amycolatopsis pithecelloba sp. nov., a novel actinomycete isolated from roots of Pithecellobium dulce in Thailand.

An actinomycete strain RM579T isolated from roots of Pithecellobium dulce in Thailand was studied using the polyphasic taxonomic approach. The results of comparative 16S rRNA gene sequence and phylogenetic analysis showed that strain RM579T belonged to the family Pseudonocardiaceae and it was most closely related to members of the genera Amycolatopsis (≤94.5% sequence similarity) and Haloechinothrix (≤93.4% sequence similarity). A phylogenetic tree constructed by neighbor-joining method indicated that strain RM579T was positioned within the clade of the genus Amycolatopsis and formed a monophyletic cluster with Amycolatopsis taiwanensis 0345M-7T, Amycolatopsis pigmentata TT00-43T and Amycolatopsis helveola TT99-32T. Strain RM579T formed white aerial mycelium and yellowish-brown substrate mycelium that fragments into rod-shaped elements. Morphological features and chemotaxonomic characteristics of strain RM579T were consistent with those of the genus Amycolatopsis. The cell wall of strain RM579T contained meso-diaminopimelic acid. Arabinose, galactose, mannose, and ribose were detected as whole-cell sugars. Mycolic acids were absent. The acyl type of the muramic acid in the cell wall was N-acetyl. Diphosphatidylglycerol, hydroxyl-phosphatidylethanolamine, phosphatidylinositol, and an unidentified phospholipid were detected as polar lipids. The major cellular fatty acids (>10%) were iso-C16:0, iso-C16:0 2-OH, and C16:1 cis9. The resultant data indicated that strain RM579T should be classified as representative of a novel species in the genus Amycolatopsis, for which the name Amycolatopsis pithecelloba sp. nov. is proposed. The type strain is RM579T (=TBRC 1849T =NBRC 106096T).

Micromonospora musae sp. nov., an endophytic actinomycete isolated from roots of Musa species

Two novel actinobacterial strains, MS1-9T and NGC1-4, were isolated from roots of Musa (ABB) cv. ‘Kluai Namwa’, collected from Chachoengsao province, and Musa (ABB) cv. ‘Kluai Chang’, from Suphan Buri province, Thailand, respectively. Comparative analysis of 16S rRNA gene (98.0 to 98.9% similarity), gyrase subunit B (gyrB) gene and whole-genome sequences emphasised that the strains MS1-9T and NGC1-4 showed closely related with Micromonospora peucetia DSM 43363T, M. krabiensis JCM 12869T and M. avicenniae DSM 45758T, respectively. Strains MS1-9T and NGC1-4 contained meso-diaminopimelic acid in cell-wall peptidoglycan. Whole-cell sugars were glucose, xylose, mannose, and ribose. The acyl type of peptidoglycan was glycolyl. MK-10(H6), MK-9(H6), and MK-10(H8) were presented as the major menaquinones. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, and phosphatidylinositol were detected as predominant phospholipid profiles. The major cellular fatty acids consisted of iso-C15:0, anteiso-C15:0, anteiso-C17:0, iso-C17:0 and C17:0. The DNA G+C content of strains MS1-9T and NGC1-4 were 72.2 and 72.3mol%, respectively. Draft genome sequences indicated by ANI values and digital DNA-DNA hybridisation analysis asserted that the strains MS1-9T and NGC1-4 should be represented as a novel species within the genus Micromonospora for which the name Micromonospora musae sp. nov. is proposed. The type strain is MS1-9T (=JCM 32149T=TISTR 2659T).

Differential occurrence of lysine 2-hydroxyisobutyrylation in psoriasis skin lesions

Lysine 2-hydroxyisobutyrylation is a newly discovered posttranslational modification. Although this modification is an important type of protein acylation, its role in psoriasis remains unstudied. We compared lesional and nonlesional psoriasis skin samples from 45 psoriasis patients. The result showed that this highly conserved modification was found in large quantities in both normal and diseased dermal tissues. However, there were a number of clear and significant differences between normal and diseased skin tissue. By comparing, lysine 2-hydroxyisobutyrylation was upregulated at 94 sites in 72 proteins and downregulated at 51 sites in 44 proteins in lesional skin. In particular, the sites with the most significant downregulation of lysine 2-hydroxyisobutyrylation were found in S100A9 (ratio = 0.140, p-value = .000371), while the most upregulated site was found in tenascin (ratio = 3.082, p-value = .0307). Loci associated with psoriasis, including FUBP1, SERPINB2 and S100A9, also exhibited significant regulation. Analyses of proteome data revealed that SERPINB2 and S100A9 were differentially expressed proteins. And bioinformatics analysis suggest that the P13K-Akt signaling pathway was more enriched with lysine 2-hydroxyisobutyrylation in lesional psoriasis skin. Our study revealed that lysine 2-hydroxyisobutyrylation is broadly present in psoriasis skin, suggesting that this modification plays a role in psoriasis pathogenesis. SignificanceA newly discovered protein posttranslational modification, lysine 2-hydroxyisobutyrylation, has been found to occur in a wide variety of organisms and to participate in some important metabolic processes. In this study, lysine 2-hydroxyisobutyrylation in lesional psoriasis skin and nonlesional psoriasis skin was quantified and compared for the first time. We found a number of differentially modified proteins and sites in our comparisons. Interestingly, some of the identified proteins and pathways with significantly different modifications, such as S100A9 and the PI3K-Akt signaling pathway, have been previously reported to be associated with psoriasis. We hope that this research will provide new insights into psoriasis.

Micromonospora caldifontis sp. nov., isolated from hot spring soil.

A single spore forming actinomycete, designated strain HSS6-8T, was isolated from a sample of hot spring soil. The strain had the chemotaxonomic properties consistent with its classification in the genus Micromonospora. The strain was found to have meso-diaminopimelic acid in the cell-wall peptidoglycan. The acyl type of the cell-wall muramic acid was glycolyl. The reducing sugars in the cell hydrolysates were glucose, arabinose, xylose, ribose, mannose, galactose and rhamnose. The phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphoglycolipid. The major menaquinones were MK-10(H6) and MK-10(H4). The major cellular fatty acids were iso-C16 : 0, anteiso-C17 : 0, C17 : 0 and anteiso-C15 : 0. The G+C content of the genomic DNA was 70.5 mol%. 16S rRNA gene sequence analysis revealed that strain HSS6-8T was closely related to Micromonospora nigra DSM 43818T (98.2 %), Micromonospora eburnea DSM 44814T (98.2 %) and Micromonospora spongicola S3-1T (98.1 %). The physiological and DNA-DNA hybridization data allowed the differentiation of strain HSS6-8T from its related species. Thus, the strain represents a novel species of the genus Micromonospora, for which the name Micromonospora caldifontis sp. nov. is proposed. The type strain is HSS6-8T (=TBRC 8927T=JCM 17126T).

Succinylation Is a Gain-of-Function Modification in Human Lens αB-Crystallin.

Acylation of lysine residues is a common post-translational modification of cellular proteins. Here, we show that lysine succinylation, a type of acylation, occurs in human lens proteins. All of the major crystallins exhibited Nε-succinyllysine (SuccK) residues. Quantification of SuccK in human lens proteins (from donors between the ages of 20 and 73 years) by LC-MS/MS showed a range between 1.2 and 14.3 pmol/mg lens protein. The total SuccK levels were slightly reduced in aged lenses (age > 60 years) relative to young lenses (age < 30 years). Immunohistochemical analyses revealed that SuccK was present in epithelium and fiber cells. Western blotting and immunoprecipitation experiments revealed that SuccK is particularly prominent in αB-crystallin, and succinylation in vitro revealed that αB-crystallin is more prone to succinylation than αA-crystallin. Mass spectrometric analyses showed succinylation at K72, K90, K92, K166, K175, and potentially K174 in human lens αB-crystallin. We detected succinylation at K72, K82, K90, K92, K103, K121, K150, K166, K175, and potentially K174 by mass spectrometry in mildly succinylated αB-crystallin. Mild succinylation improved the chaperone activity of αB-crystallin along with minor perturbation in tertiary and quaternary structure of the protein. These observations imply that succinylation is beneficial to αB-crystallin by improving its chaperone activity with only mild conformational alterations.

Microbacterium suaedae sp. nov., isolated from Suaeda aralocaspica.

Two bacterial strains, YZYP 306T and YZGP 509, were isolated from the halophyte Suaeda aralocaspica collected from the southern edge of the Gurbantunggut desert, north-west China. Cells were Gram-stain-positive, aerobic, non-motile, short rods. Strain YZYP 306T grew at 4-40 °C, while strain YZGP 509 grew at 4-42 °C, with optimum growth at 28 °C, and they both grew at pH 6.0-12.0 and 0-15 % (w/v) NaCl. Phylogenetic analyses of the 16S rRNA gene sequences placed the two strains within the genus Microbacterium with the highest similarities to Microbacterium indicum BBH6T (97.8 %) and Microbacterium sorbitolivorans SZDIS-1-1T (97.2 %). The average nucleotide identity value between YZYP 306T and M. indicum BBH6T was 78.3 %. The genomic DNA G+C contents of strains YZYP 306T and YZGP 509 were 68.49 and 68.53 mol%, respectively. The characteristic cell-wall amino acid was ornithine. Whole-cell sugars were galactose, mannose and ribose. The acyl type of the peptidoglycan was glycolyl. The major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The major menaquinones were MK-10 and MK-11. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, an unidentified phospholipid and an unidentified glycolipid. These results are consistent with the classification of the two strains into the genus Microbacterium. On the basis of the evidence presented in this study, strains YZYP 306T and YZGP 509 are representatives of a novel species in the genus Microbacterium, for which the name Microbacterium suaedae sp. nov. is proposed. The type strain is YZYP 306T (=CGMCC 1.16261T=KCTC 49101T).

Planctomonas deserti gen. nov., sp. nov., a new member of the family Microbacteriaceae isolated from soil of the Taklamakan desert.

A Gram-staining-positive, aerobic, irregular coccoid- to ovoid-shaped, non-spore-forming and motile bacterium, designated strain 13S1-3T, was isolated from a soil sample from the rhizosphere of Tamarix collected in the Taklamakan desert in Xinjiang Uygur Autonomous Region, PR China. The strain was examined by a polyphasic approach to clarify its taxonomic position. Strain 13S1-3T grew optimally at 28-30 °C, pH 7.0 and with 0-1 % (w/v) NaCl. The cell-wall peptidoglycan was of the B2γ type and contained d-alanine, d-glutamic acid, glycine, d-2,4-diaminobutyric acid and l-2,4-diaminobutyric acid. Ribose, xylose, glucose and galactose were detected as cell-wall sugars. The acyl type of the muramic acid was acetyl. The predominant menaquinones were MK-12, MK-11, MK-13 and MK-10. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, two unidentified glycolipids and one unidentified phospholipid. The major whole-cell fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The DNA G+C content was 70.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that 13S1-3T represented a member of the family Microbacteriaceae and showed the highest level of 16S rRNA gene sequence similarity with Frondihabitans australicus E1HC-02T (97.11 %). Phylogenetic trees revealed that 13S1-3T formed a distinct lineage with respect to closely related genera within the family Microbacteriaceae. On the basis of the results of phylogenetic, phenotypic and chemotaxonomic analyses, 13S1-3T is distinguishable from phylogenetically related genera in the family Microbacteriaceae, and represents a novel species of a new genus, for which the name Planctomonas deserti gen. nov., sp. nov. is proposed. The type strain is 13S1-3T (=KCTC 49115T=CGMCC 1.16554T).

Allorhizocola rhizosphaerae gen. nov., sp. nov., a new member of Micromonosporaceae isolated from rhizosphere soil of the plant Calligonum mongolicum.

The taxonomic position of an actinobacterium, designated CPCC 204380T, which was isolated from a rhizosphere soil sample of the plant Calligonum mongolicum collected from Xinjiang Province, China, was established using a polyphasic approach. Vegetative hyphae developed well and globose bodies formed from aged hyphae. Spore chains that differentiated from the vegetative hyphae contained non-motile rod-shaped spores. The peptidoglycan contained meso-diaminopimelic acid and 3-hydroxydiaminopimelic acid as the diagnostic amino acids. The acyl type of the peptidoglycan was glycolyl. Glucose, mannose, ribose and xylose were detected in whole-cell hydrolysates. The predominant menaquinone was MK-10(H8), followed by MK-10(H6) and MK-10(H4). The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The major fatty acids were iso-C15 : 0, iso-C16 : 0 and C17 : 1ω9c. The genomic G+C content was 64.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CPCC 204380T should be placed in the family Micromonosporaceae, in which it formed a distinct lineage next to the genera Rhizocola, Catellatospora, Catelliglobosispora, Hamadaea and Allocatelliglobosispora. It shared the highest 16S rRNA gene sequence similarities with Rhizocola hellebori K12-0602T (96.1 %), Catellatospora chokoriensis 2-25/1T (95.9 %), Catelliglobosispora koreensis DSM 44566T (95.9 %), Hamadaea tsunoensis DSM 44101T (95.3 %) and Allocatelliglobosispora scoriae Sco-B14 T (94.2 %), and less than 94.0 % sequence similarity with other validly described species. The combination of phylogenetic analysis and phenotypic characteristics supported the proposal of strain CPCC 204380T as representing a novel species of a new genus in the family Micromonosporaceae, for which the name Allorhizocola rhizosphaerae gen. nov., sp. nov. is proposed. CPCC 204380T (=DSM 102292T=KCTC 39746 T) is the type strain of the type species.

Jishengella zingiberis sp. nov., isolated from root tissue of Zingiber montanum.

A novel actinomycete, strain PLAI 1-1T, which formed spiny single spore directly on substrate mycelium was isolated from root tissue of Zingiber montanum. The isolate contained meso-diaminopimelic acid and 3-hydroxydiaminopimelic acid in the cell-wall peptidoglycan. The acyl type of the cell-wall muramic acid was glycolyl. The whole-cell sugars of strain PLAI 1-1T were glucose, arabinose, xylose, ribose and a trace amount of mannose. The membrane phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine and phosphatidylinositol. The major menaquinone was MK-9 (H4). The main cellular fatty acids were iso-C15 : 0 and C17 : 1ω8c. The G+C content of the genomic DNA was 70.6 mol%. 16S rRNA gene sequence analysis revealed that strain PLAI 1-1T was a member of the genus Jishengella and had the highest 16S rRNA gene sequence similarity to Jishengella endophytica DSM 45430T (99.2 %). Based on the data of physiological and biochemical tests, including the result of DNA-DNA hybridization, strain PLAI 1-1T represents a novel species of the genus Jishengella, for which the name Jishengellazingiberis sp. nov. is proposed. The type strain is PLAI 1-1T (=TBRC 7644T=NBRC 113144T).

Ultradeep Palmitoylomics Enabled by Dithiodipyridine-Functionalized Magnetic Nanoparticles.

Palmitoylation, a type of fatty acylation, has vital roles in many biological processes. For ultradeep identification of protein palmitoylation, an enrichment approach based on a novel magnetic microsphere modified with 2,2'-dithiodipyridine (Fe3O4/SiO2-SSPy microsphere) is presented in this study. The Fe3O4/SiO2-SSPy microspheres were synthesized by directly coating thiol-containing silane coupling agent onto the magnetic supraparticles in aqueous solution at room temperature. Due to the intrinsic magnetic properties, high surface-to-volume ratios, and abundant reactive functional groups on the surface, these microspheres enabled direct capture of palmitoylated targets and convenient isolation, contributing to remarkable enrichment selectivity (purifying palmitoylated peptides from mixtures with nonpalmitoylated peptides even at a 1:500 molar ratio) and sensitivity (the detection limit was at femtomole level), thus enabling a global annotation of protein palmitoylation for complex biological samples. We successfully identified 1304 putative palmitoylated proteins from mouse brain tissues by using this method, which is the largest mouse palmitoylome data set to date. Except for those known members, many new proteins and pathways were also found to be regulated by palmitoylation.

Isolation and characterization of Corynebacterium spp. from bulk tank raw cow's milk of different dairy farms in Germany.

We detected Corynebacterium spp. in raw milk samples of three farms by means of a selective, tellurite-containing medium. The isolated strains were identified based on full 16S rRNA gene sequences and partial rpoB gene sequences as C. xerosis, C. variabile, C. lactis, C. callunae, C. confusum, C. glutamicum and C. crudilactis. The identification based on 16S rRNA and rpoB sequences was not reliable for isolates of C. xerosis. Chemotaxonomic markers of the isolates, fatty acids, acyl type of peptidoglycan, presence and length of mycolic acids, quinone patterns, and polar lipids, were in accord with the known characteristics of these species. Biochemical profiles, analyzed with the API Coryne system, were able to differentiate all groups, but were unable to identify the strains due to an inappropriate database for raw-milk associated corynebacteria. Most of the tested isolates showed a single-substance resistance against oxacillin, but three single isolates were classified as multidrug resistant.

LC\u2013MS/MS-based quantitative study of the acyl group- and site-selectivity of human sirtuins to acylated nucleosomes

Chromatin structure and gene expression are dynamically regulated by posttranslational modifications of histones. Recent advance in mass spectrometry has identified novel types of lysine acylations, such as butyrylation and malonylation, whose functions and regulations are likely different from those of acetylation. Sirtuins, nicotinamide adenine dinucleotide (NAD+)-dependent histone deacetylases, catalyze various deacylations. However, it is poorly understood how distinct sirtuins regulate the histone acylation states of nucleosomes that have many lysine residues. Here, we provide mass spectrometry-based quantitative information about the acyl group- and site-selectivity of all human sirtuins on acylated nucleosomes. The acyl group- and site-selectivity of each sirtuin is unique to its subtype. Sirt5 exclusively removes negatively-charged acyl groups, while Sirt1/2/3/6/7 preferentially remove hydrophobic acyl groups; Sirt1 and Sirt3 selectively remove acetyl group more than butyryl group, whereas Sirt2 and Sirt6 showed the opposite selectivity. Investigating site-selectivity for active sirtuins revealed acylated lysines on H4 tails to be poor substrates and acylated H3K18 to be a good substrate. Furthermore, we found Sirt7 to be a robust deacylase of H3K36/37, and its activity reliant on nucleosome-binding at its C-terminal basic region. All together, our quantitative dataset provides a useful resource in understanding chromatin regulations by histone acylations.

ANTHOCYANIN, THE NATURAL COLORANT AND ITS IMPLICATIONS IN HEALTH AND FOOD INDUSTRY: A SEARCH

Anthocyanins are unique plant pigments since they are critical for most of the red, purple and blue pigmentation of flowers, fruits and vegetables. Meanwhile, they are reactive in nature, anthocyanins degrade easily, or react with other compounds such as reactive metals such as iron, aluminum, and tin in the media, toform colorless or brown colored by products. Anthocyanins are glycosides of anthocyanidins (aglycones) and sugars. Anthocyanidins are almost always glycosylated in the 3-position, though glycosylation in other positions and in more than one position at a time is also encountered. Furthermore, the sugar moiety may be acylated with aliphatic or aromatic acids. Anthocyanidins are less in number but anthocyanins show much diversity offered by glycosylation and acylation. 635 anthocyanins were identified in nature, featuring six common aglycones and various types of glycosylations and acylations. Reports suggest that dietary consumption of anthocyanins is good for health. Based upon many cell-line studies, animal models, and human clinical trials, it has been suggested that anthocyanins possess anti-inflammatory and anticarcinogenic activity, cardiovascular disease prevention, obesity control, and diabetes alleviation properties,all of which are more or less associated with their potent antioxidant property. Evidence suggests that absorption of anthocyanins occurs in the stomach and small intestine. Epithelial tissue uptake seems to be highly efficient, yet transportation into circulation, tissue distribution, and urine excretion are very limited.The bioactivity of bioavailable anthocyanins should be a focus of future research regarding their putative health-promoting effects.

Microbacterium hibisci sp. nov., isolated from rhizosphere of mugunghwa (Hibiscus syriacus L.).

A Gram-stain-positive, aerobic, non-motile, short-rod shaped actinobacterium, designated THG-T2.14T, was isolated from soil sampled from the rhizosphere of mugunghwa. Growth occurred at 10-40 °C (optimum 30 °C), at pH 5.0-10.0 (optimum 7.0) and at 0-7.0 % NaCl (optimum 3.0 %). Based on 16S rRNA gene sequence analysis, the nearest phylogenetic neighbours of strain THG-T2.14T were identified as Microbacterium yannicii DSM 23203T (98.8 %), Microbacterium trichothecenolyticum DSM 8608T (98.8 %), Microbacterium arthrosphaerae DSM 22421T (98.7 %) and Microbacterium jejuense KACC 17124T (98.4 %). The major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, one unidentified lipid, two unidentified phospholipids and two unidentified phosphoglycolipids. The menaquinones were MK-12, and MK-13. The major polyamine was spermidine. The peptidoglycan contained ornithine, alanine, glycine, homoserine and glutamic acid. The diagnostic diamino acid was ornithine. The acyl type of the muramic acid was glycolyl. The whole-cell sugars were rhamnose, ribose, galactose, arabinose, xylose and glucose. The DNA G+C content of strain THG-T2.14T was 71.2 mol%. The DNA-DNA relatedness between strain THG-T2.14T and its closest reference strains were significantly lower than the threshold value of 70 %. On the basis of the phylogenetic analysis, chemotaxonomic data, physiological characteristics and DNA-DNA hybridization data, strain THG-T2.14T represents a novel species of the genus Microbacterium, for which the name Microbacterium hibisci sp. nov. is proposed. The type strain is THG-T2.14T (=KACC 18931T=CCTCC AB 2016180T).

Acid Fluorides as Acyl Electrophiles in Suzuki–Miyaura Coupling

The first palladium‐catalyzed construction of ketones through Suzuki–Miyaura reaction by using acid fluorides is described. In contrast to typical acyl electrophiles such as acid chlorides, acid fluorides are uncommon acyl electrophiles to use in boron‐based coupling reactions, probably due to a high level of stability toward nucleophiles. This first attempt to use acid fluorides as a coupling partner with boronic acids allowed highly functional group tolerance and a wide substrate scope while affording various ketones in effective yields.

First comprehensive proteome analysis of lysine crotonylation in seedling leaves of Nicotiana tabacum

Histone crotonylation is a new lysine acylation type of post-translational modification (PTM) enriched at active gene promoters and potential enhancers in yeast and mammalian cells. However, lysine crotonylation in nonhistone proteins and plant cells has not yet been studied. In the present study, we performed a global crotonylation proteome analysis of Nicotiana tabacum (tobacco) using high-resolution LC-MS/MS coupled with highly sensitive immune-affinity purification. A total of 2044 lysine modification sites distributed on 637 proteins were identified, representing the most abundant lysine acylation proteome reported in the plant kingdom. Similar to lysine acetylation and succinylation in plants, lysine crotonylation was related to multiple metabolism pathways, such as carbon metabolism, the citrate cycle, glycolysis, and the biosynthesis of amino acids. Importantly, 72 proteins participated in multiple processes of photosynthesis, and most of the enzymes involved in chlorophyll synthesis were modified through crotonylation. Numerous crotonylated proteins were implicated in the biosynthesis, folding, and degradation of proteins through the ubiquitin-proteasome system. Several crotonylated proteins related to chromatin organization are also discussed here. These data represent the first report of a global crotonylation proteome and provide a promising starting point for further functional research of crotonylation in nonhistone proteins.

Synthetic Chromatin Acylation by an Artificial Catalyst System

Summary Histone acetylation is physiologically regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs) and constitutes a fundamental regulatory element in gene expression. New types of lysine acylation on histones have recently been identified, but it remains unclear how chromatin function is regulated by divergent types of histone acylation and various enzymes. Here, we report on an approach to modulating histone acylation states synthetically without relying on enzymes. We have developed an artificial catalyst system composed of nucleosome-binding catalysts and acyl donors, which preferentially acetylated or malonylated lysines on histone tails and suppressed intra- and inter-nucleosome interactions similarly to HATs. We demonstrate the utility of our approach by identifying a site-selectivity difference between two HDAC isoforms, Sirt1 and Sirt6, and comparing the functions of histone malonylation and acetylation. Our system is applicable to endogenous chromatin without genetic manipulation; thus, it can be used to dissect the complex regulation of chromatin.